Brain metastases occur in approximately 15% of breast cancer patients and confer a dismal prognosis. Brain metastases are thought to increasing as a sanctuary site, as systemic control of breast cancer metastases improves. We are conducting microarray analysis of surgically resected brain metastases of breast cancer, using laser capture microdissection, amplification and 30K cDNA arrays. These data are being compared to a cohort of unmatched primary breast tumors, matched for histopathology, TNM and grade. Preliminary data indicate that brain metastases differ from primary tumors in many respects, including the expression of oncogenes, angiogenesis markers, proliferative markers, apoptotic markers and signaling pathways. This information will ultimately be validated in transfection assays.